P212121

In true end of the year originality here are 10 favorites from 2009:

1) Best Online Introductions to Crystallography

2) Scientific Research in 10 Simple Rules

3) Free Crystallographic Space Group Diagrams and Symbols

4) Ultimate List of Protein Crystallization Resources

5) Scientific Presentation Resources

6) 17 Structural Journals with RSS

7) Ultimate List on Cryocrystallography & Radiation Damage

Covering your Tracks

9) 10 Ways to Comfort a Crystallographer

10) Top 5 Lies of Principle Investigators

10 questions to consider before setting up protein crystallization trials:

1) How pure is your protein sample?

2) What chemicals are present in the protein buffer?

3) Is the protein modified such as phosphorylated, glycosylated or methylated?

4) What temperature and pH is the protein stable?

5) What concentration causes the protein to precipitate out of solution?

6) Does the protein have any known substrates, metals, inhibitors or ligands?

7) Have related proteins been crystallized?

Is the protein sensitive to proteolysis?

9) Does the protein have cysteines?

10) How has the protein been stored?

Feel free to add any questions that you consider in the comments.

I wanted to take a moment to wish all those celebrating this time of year, all the best!

Thanks to everyone for your support and encouragement this year. I am constantly amazed at all the visits, comments, emails, and phone calls.

I truly appreciate all those that have helped to make this site better.

The repetitive nature of editing a PDB file can consume hours of your time and leave you feeling unfulfilled.

What if you could simply and quickly edit a PDB file without hacking together a solution using vim?

The PDB Editor has the ability to do just that and can be downloaded here for free! The manual is really great in that it explains the program’s various functions using screen shots.

The ability to delete certain aspects of a PDB file would have saved me so much time the past, it’s sick.


You can also edit secondary structure which can be outputted into PDB format.


Happy editing!

X-ray crystallography in a basic sense studies the result of photons interacting with electrons.

How do we describe how photons are reflected?

Richard Feynman won the Nobel Prize in Physics in 1965 for fundamental work in quantum electrodynamics.

Vega Science has put together a series lectures that Richard give at the University of Auckland in 1978.

Below is a time line with a couple of notes from his 77 minute lecture entitled:
Part 1: Photons – Corpuscles of Light

00:00 Introduction
04:40 Light
09:35 Theory of interaction with light
14:42 Great analogy between checkers and nature
20:20 Explains the theory
23:15 ‘I enjoyed your lecture, but didn’t understand it’
26:15 ‘Nobody understands it’
33:13 Possible meaning
34:45 Describes theory
40:48 Reflection
47:50 Science is based on probabilities
57:10 Answer to the reflection Problem
68:10 Questions

The lecture makes me wonder about the relationship between protein crystal size and the probability of photons being diffracted. I am starting to get uneasy about how much is explained away due to crystal packing.

If you need to mutate multiple residues simultaneously there is a great option to use in Coot instead of mutating them individually.

Calculate -> Mutate Residue Range…


1) Make sure you are mutating the correct PDB file
2) Select Chain
3) Enter the residues range by number that you would like mutated
4) Enter desired sequence
5) Option for to autofit the mutated residues (you need to have a map for this)

What are some of the possible uses?

1) Create a poly-alanine chain
2) Mutate a structure that varies between species
3) Mutate hyper variable regions

Note: You cannot add residues with this option.

I had the pleasure of taking my first crystallography course from Dr. Cora Lind. Cora was kind enough to ask me to speak at the American Crystallography Association meeting this year. In addition, she has always been patient and helpful with my crystallography questions.

Recently, Cora arranged for the video taping of her crystallography course.

I have not yet watched all the videos (in total they run nearly 23 hours!), but feel comfortable recommending them since I took the course. Also there are copies of the slides from each lecture to make it easy to follow along at home.

The relevance of the introductory lecture made me smile, ‘you may find publications with crystal data that may not make sense… you need to be able to judge that.’

I am really grateful for Cora putting this lecture series together.

If you find this video series helpful or think the crystallographic community would benefit from more lectures being posted, please drop a comment. Thanks.

The University of Alabama at Birmingham (UAB) requested on Dec. 8th for the removal of 12 structures from the PDB. The 12 structures are spread across 9 journals including Nature, Cell and the Journal of Molecular Biology.

Here are some highlights from the request concerning these structures:

1BEF is a synthetic version of 1JXP (I wrote about 1NS3 being the structure used, 1JXP and 1NS3 contain the same origin, orientation, space group and unit cell).

My favorite:
1CMW had its B factors derived by subtracting 16.00 from values found in the structure 1TAQ

1DF9 which replaced 2QID with the update including the removal of 155 waters some of which had hydrogren bonding distances less than 1 Angstrom.

1G40 is without any water despite diffracting to 2 Angstroms also there is a strange update to the unit cell parameters in Feb. of 2007 (fits into the time line previously posted)

1G44 contains 36 chemically impossible close contacts

1L6L has either 2036 residues or 2366 residues, 1011 waters or 1522 waters, etc…

2OU1 also involved heavy drinking

1RID and 1Y8E contain poor geometry, strange B factors and very high solvent content

2A01 has great electron density that correspond to physically impossible features

2HR0 has already been trashed.
————–

I noted that there were 449 citations that referred to these dubious publications on Dec. 10th. A week has passed since the original request made by UAB. Currently, only 1 structure (1BEF) along with the corresponding paper has been retracted. Now according to Google Scholar, not even a week later, 6 more citations have been added.

I hope that other publishers are able to review the data involving these structures quickly and act accordingly as to prevent the further spread of inaccurate information.

Note: there is going to be a delay from when this information was announced to when papers (patents, books, etc) work their way through the system, but the sooner the better

A fresh perspective on a project can be helpful, however, as a graduate student be careful with your new ideas. You can have the most brilliant idea, but you are in a world of limited resources.

Instead, focus on getting stuff done.

Join a lab and start reducing the workload of your colleagues. We don’t need new ideas for other people to work on.

“Imagination is more important than knowledge.” Albert Einstein
Getting results is more important than both.

is a good idea if you think people are on to you. Eric points us to the communication in Nature that brought into question PDB entry 2HR0 (background posts: here and here). The reply was also published in Nature with the authors standing by their data. The 30-40 Angstrom gaps are explained by citing a personal communication with W. A. Hendrickson as well as the presence of protein fragments that serve as disordered lattice contacts.

The possible location of the protein fragment is shown in the reply.
Below is a display of the protein packing without the ‘protein fragments’ that served as the lattice contacts.

The figure below, shows additional symmetry related proteins, gaps occur vertically (in the c-direction) and are noted with a red circle.

Artem notes that they could have done a better job fabricating the data. We all Most of us try to learn from our mistakes and correct them, if possible.

Learning from your mistakes:

A glaring problem with the 2HR0 structure was the existence of these gaps. You can come to your conclusions on whether you believe there are disordered lattice contacts. However, what would greatly undermine their credibility would be if they had deposited another structure that contained these unusual gaps.

This brings us to the structure 2OU1, but wait. This structure doesn’t have very large gaps…
They learned.

If you take a close look at the PDB entry you will notice that this structure was updated (see Deposition Summary: right side, under the picture of the molecule). The structure that was initially deposited with the PDB entry 1L6K.

Here is the textual comparison:

The major change is shown with the red arrow above noting that the c-axis was nearly cut in half.

Why update?

Covering their Tracks:

The crystal packing of 1L6K:
The gaps… ~30 Angstroms, sound familiar?

The crystal packing of 2OU1:
The gaps have been significantly reduced.

They learned from their mistake in the 2HR0 entry. The large reduction in the length of the c-axis results in more reasonable crystal packing.

Time line:

The PDB entry 2HR0 was initially released at the end of October in 2006. The initial correspondence questioning the structure and reply were published in August 2007.

The original structure PDB entry 1L6K was deposited in 2002. The update of this structure was in February of 2007. It would be interesting to know when the authors were contacted about 2HR0.

One explanation is that once they were contacted about the 2HR0 structure, they realized there was a similar issue with 1L6K and replaced it with 2OU1.

As with the hypothesis about the entry 1BEF, I do not have any proof that this is what is going on, but definitely thought it was worth mentioning.

What do you think? Sound reasonable?